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RBM6 RNA binding motif protein 6 [ Homo sapiens (human) ]

Gene ID: 10180, updated on 3-Nov-2024

Summary

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Official Symbol
RBM6provided by HGNC
Official Full Name
RNA binding motif protein 6provided by HGNC
Primary source
HGNC:HGNC:9903
See related
Ensembl:ENSG00000004534 MIM:606886; AllianceGenome:HGNC:9903
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
3G2; g16; DEF3; DEF-3; HLC-11; NY-LU-12
Summary
Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in endometrium (RPKM 33.9), lymph node (RPKM 31.2) and 25 other tissues See more
Orthologs
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Genomic context

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See RBM6 in Genome Data Viewer
Location:
3p21.31
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (49940150..50077249)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (49969226..50106392)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (49977583..50114682)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49934943-49935443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49939657-49940330 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49940331-49941004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19881 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49941679-49942351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19883 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49949147-49949724 Neighboring gene macrophage stimulating 1 receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14377 Neighboring gene MON1 homolog A, secretory trafficking associated Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49977213-49977735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49977736-49978257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14379 Neighboring gene NANOG hESC enhancer GRCh37_chr3:50050258-50050926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50119658-50120158 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:50120996-50121560 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50126209-50126800 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50126801-50127391 Neighboring gene MPRA-validated peak4650 silencer Neighboring gene RBM5 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50157731-50158609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50158610-50159487 Neighboring gene RNA binding motif protein 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50160473-50160973 Neighboring gene SEMA3F antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50162997-50163986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50170449-50170950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50172709-50173300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50177671-50178232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50178233-50178794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50188081-50188752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14380 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14381 Neighboring gene basic proline-rich protein-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14382 Neighboring gene semaphorin 3F

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RBM6 splicing factor promotes homologous recombination repair of double-strand breaks and modulates sensitivity to chemotherapeutic drugs.
    Title: RBM6 splicing factor promotes homologous recombination repair of double-strand breaks and modulates sensitivity to chemotherapeutic drugs.
  2. RNA-binding protein RBM6 acts as a tumor suppressor gene to inhibit the progression of hepatocellular carcinoma.
    Title: RNA-binding protein RBM6 acts as a tumor suppressor gene to inhibit the progression of hepatocellular carcinoma.
  3. RNA-Binding Motif Protein 6 is a Candidate Serum Biomarker for Pancreatic Cancer
    Title: RNA-Binding Motif Protein 6 is a Candidate Serum Biomarker for Pancreatic Cancer.
  4. Upregulation of RBM6 reduced the expression of EGFR, ERK and p-ERK in vitro and in vivo. Data suggest that RBM6 as a tumor suppressor represses the growth and progression in laryngocarcinoma.
    Title: RNA-binding protein RBM6 as a tumor suppressor gene represses the growth and progression in laryngocarcinoma.
  5. Antagonizes the effects of RBM5, RBM6, and RBM10 in cell colony formation.
    Title: RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation.
  6. RBM6 mRNA experiences altered co-transcriptional gene regulation in certain cancers. RBM6-RBM5 transcription-induced chimerism might be a process that is linked to the tumour-associated increased transcriptional activity of the RBM6 gene
    Title: RBM6-RBM5 transcription-induced chimeras are differentially expressed in tumours.
  7. identified a novel fusion of the RNA binding motif 6 (RBM6) gene to CSF1R gene generated presumably by a t(3;5)(p21;q33) translocation that induced a myeloid proliferative disease with features of megakaryoblastic leukemia in a murine transplant model
    Title: A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ36517, FLJ39446, FLJ42036, DKFZp686B0877

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding TAS
Traceable Author Statement
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
RNA-binding protein 6
Names
RNA-binding protein DEF-3
lung cancer antigen NY-LU-12
lung cancer protooncogene 11

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001167582.2 → NP_001161054.1  RNA-binding protein 6 isoform 2

    See identical proteins and their annotated locations for NP_001161054.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks several internal exons in the CDS, as compared to variant 1. This results in a downstream in-frame AUG start codon, and the resulting isoform (2) has a shorter N-terminus, as compared to isoform 1. Variants 2, 3, 4, 5, and 6 all encode the same isoform (2).
    Source sequence(s)
    AK291719, BC012112, BC046643
    Consensus CDS
    CCDS54586.1
    UniProtKB/TrEMBL
    B3KSK6
    Related
    ENSP00000393530.1, ENST00000442092.5
    Conserved Domains (3) summary
    cd12563
    Location:132 → 218
    RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
    cd16163
    Location:244 → 303
    OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
    pfam01585
    Location:529 → 573
    G-patch; G-patch domain

  2. NM_001349190.2 → NP_001336119.1  RNA-binding protein 6 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3), as well as variants 2, 4, 5, and 6, encodes isoform 2.
    Source sequence(s)
    AC104450, AC105935
    Consensus CDS
    CCDS54586.1
    UniProtKB/TrEMBL
    B3KSK6
    Related
    ENSP00000392939.1, ENST00000422955.5
    Conserved Domains (3) summary
    cd12563
    Location:132 → 218
    RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
    cd16163
    Location:244 → 303
    OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
    pfam01585
    Location:529 → 573
    G-patch; G-patch domain

  3. NM_001349191.2 → NP_001336120.1  RNA-binding protein 6 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4), as well as variants 2, 3, 5, and 6, encodes isoform 2.
    Source sequence(s)
    AC104450, AC105935
    Consensus CDS
    CCDS54586.1
    UniProtKB/TrEMBL
    B3KSK6
    Conserved Domains (3) summary
    cd12563
    Location:132 → 218
    RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
    cd16163
    Location:244 → 303
    OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
    pfam01585
    Location:529 → 573
    G-patch; G-patch domain

  4. NM_001349192.2 → NP_001336121.1  RNA-binding protein 6 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5), as well as variants 2, 3, 4, and 6, encodes isoform 2.
    Source sequence(s)
    AC104450, AC105935
    Consensus CDS
    CCDS54586.1
    UniProtKB/TrEMBL
    B3KSK6
    Conserved Domains (3) summary
    cd12563
    Location:132 → 218
    RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
    cd16163
    Location:244 → 303
    OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
    pfam01585
    Location:529 → 573
    G-patch; G-patch domain

  5. NM_001349193.2 → NP_001336122.1  RNA-binding protein 6 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6), as well as variants 2, 3, 4, and 5, encodes isoform 2.
    Source sequence(s)
    AC104450, AC105935
    Consensus CDS
    CCDS54586.1
    UniProtKB/TrEMBL
    B3KSK6
    Conserved Domains (3) summary
    cd12563
    Location:132 → 218
    RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
    cd16163
    Location:244 → 303
    OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
    pfam01585
    Location:529 → 573
    G-patch; G-patch domain

  6. NM_001349194.2 → NP_001336123.1  RNA-binding protein 6 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC104450, AC105935
    UniProtKB/TrEMBL
    B3KSK6
    Conserved Domains (4) summary
    cd12563
    Location:140 → 226
    RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
    cd16163
    Location:252 → 311
    OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
    pfam01585
    Location:537 → 581
    G-patch; G-patch domain
    cl17169
    Location:1 → 19
    RRM_SF; RNA recognition motif (RRM) superfamily

  7. NM_005777.3 → NP_005768.1  RNA-binding protein 6 isoform 1

    See identical proteins and their annotated locations for NP_005768.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF091264, AK291719, BC012112
    Consensus CDS
    CCDS2809.1
    UniProtKB/Swiss-Prot
    B4E0G6, O60549, O75524, P78332, Q86SS3
    UniProtKB/TrEMBL
    A8K6Q4
    Related
    ENSP00000266022.4, ENST00000266022.9
    Conserved Domains (5) summary
    COG1357
    Location:92 → 237
    YjbI; Uncharacterized protein YjbI, contains pentapeptide repeats [Function unknown]
    cd16163
    Location:766 → 825
    OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins
    pfam01585
    Location:1051 → 1094
    G-patch; G-patch domain
    cd12314
    Location:456 → 533
    RRM1_RBM6; RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6)
    cd12563
    Location:654 → 740
    RRM2_RBM6; RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6)

RNA

  1. NR_146071.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC104450, AK298108, BC012112
    Related
    ENST00000419610.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    49940150..50077249
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047447131.1 → XP_047303087.1  RNA-binding protein 6 isoform X1

    UniProtKB/Swiss-Prot
    B4E0G6, O60549, O75524, P78332, Q86SS3

  2. XM_047447132.1 → XP_047303088.1  RNA-binding protein 6 isoform X2

  3. XM_017005496.3 → XP_016860985.2  RNA-binding protein 6 isoform X4

    Conserved Domains (3) summary
    COG1357
    Location:92 → 237
    YjbI; Uncharacterized protein YjbI, contains pentapeptide repeats [Function unknown]
    cd12314
    Location:456 → 533
    RRM1_RBM6; RNA recognition motif 1 in vertebrate RNA-binding protein 6 (RBM6)
    cd12563
    Location:654 → 740
    RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)

  4. XM_047447137.1 → XP_047303093.1  RNA-binding protein 6 isoform X8

  5. XM_047447136.1 → XP_047303092.1  RNA-binding protein 6 isoform X8

    Related
    ENSP00000408665.1, ENST00000425608.5

  6. XM_047447133.1 → XP_047303089.1  RNA-binding protein 6 isoform X5

  7. XM_006712916.2 → XP_006712979.1  RNA-binding protein 6 isoform X3

    See identical proteins and their annotated locations for XP_006712979.1

    UniProtKB/TrEMBL
    E9PGM9
    Related
    ENSP00000396466.1, ENST00000443081.5
    Conserved Domains (5) summary
    smart00443
    Location:917 → 963
    G_patch; glycine rich nucleic binding domain
    COG1357
    Location:11 → 127
    YjbI; Uncharacterized protein YjbI, contains pentapeptide repeats [Function unknown]
    cd12314
    Location:324 → 401
    RRM1_RBM6; RNA recognition motif 1 in vertebrate RNA-binding protein 6 (RBM6)
    cd12563
    Location:522 → 608
    RRM2_RBM6; RNA recognition motif 2 in vertebrate RNA-binding protein 6 (RBM6)
    cd16163
    Location:634 → 693
    OCRE_RBM6; OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins

  8. XM_017005497.2 → XP_016860986.1  RNA-binding protein 6 isoform X6

    UniProtKB/TrEMBL
    B3KSK6

  9. XM_047447134.1 → XP_047303090.1  RNA-binding protein 6 isoform X7

  10. XM_047447135.1 → XP_047303091.1  RNA-binding protein 6 isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    49969226..50106392
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344843.1 → XP_054200818.1  RNA-binding protein 6 isoform X8

  2. XM_054344834.1 → XP_054200809.1  RNA-binding protein 6 isoform X1

    UniProtKB/Swiss-Prot
    B4E0G6, O60549, O75524, P78332, Q86SS3

  3. XM_054344835.1 → XP_054200810.1  RNA-binding protein 6 isoform X2

  4. XM_054344837.1 → XP_054200812.1  RNA-binding protein 6 isoform X4

  5. XM_054344842.1 → XP_054200817.1  RNA-binding protein 6 isoform X8

  6. XM_054344838.1 → XP_054200813.1  RNA-binding protein 6 isoform X5

  7. XM_054344836.1 → XP_054200811.1  RNA-binding protein 6 isoform X3

    UniProtKB/TrEMBL
    E9PGM9

  8. XM_054344839.1 → XP_054200814.1  RNA-binding protein 6 isoform X6

  9. XM_054344840.1 → XP_054200815.1  RNA-binding protein 6 isoform X7

  10. XM_054344841.1 → XP_054200816.1  RNA-binding protein 6 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P78332.5 GenPept UniProtKB/Swiss-Prot:P78332

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